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Small fixes #123

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Small fixes #123

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731213b
don't unnecessarily divide by r
mcocdawc Jan 15, 2025
5d4c5f7
renamed from_pyscf_molecule -> from_pyscf
mcocdawc Jan 15, 2025
b226b02
added missing rst files for pyscf
mcocdawc Jan 15, 2025
0848851
Merge branch 'master' of github.com:mcocdawc/chemcoord into small_fixes
mcocdawc Jan 19, 2025
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2 changes: 2 additions & 0 deletions docs/source/src_AsymmetricUnitCartesian/chemcoord.AsymmetricUnitCartesian.rst
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Expand Up @@ -30,6 +30,7 @@
~AsymmetricUnitCartesian.fragmentate
~AsymmetricUnitCartesian.from_ase_atoms
~AsymmetricUnitCartesian.from_pymatgen_molecule
~AsymmetricUnitCartesian.from_pyscf
~AsymmetricUnitCartesian.get_align_transf
~AsymmetricUnitCartesian.get_angle_degrees
~AsymmetricUnitCartesian.get_ase_atoms
Expand Down Expand Up @@ -70,6 +71,7 @@
~AsymmetricUnitCartesian.symmetrize
~AsymmetricUnitCartesian.to_cjson
~AsymmetricUnitCartesian.to_latex
~AsymmetricUnitCartesian.to_pyscf
~AsymmetricUnitCartesian.to_string
~AsymmetricUnitCartesian.to_xyz
~AsymmetricUnitCartesian.to_zmat
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2 changes: 2 additions & 0 deletions docs/source/src_Cartesian/chemcoord.Cartesian.rst
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Expand Up @@ -30,6 +30,7 @@
~Cartesian.fragmentate
~Cartesian.from_ase_atoms
~Cartesian.from_pymatgen_molecule
~Cartesian.from_pyscf
~Cartesian.get_align_transf
~Cartesian.get_angle_degrees
~Cartesian.get_ase_atoms
Expand Down Expand Up @@ -69,6 +70,7 @@
~Cartesian.symmetrize
~Cartesian.to_cjson
~Cartesian.to_latex
~Cartesian.to_pyscf
~Cartesian.to_string
~Cartesian.to_xyz
~Cartesian.to_zmat
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8 changes: 8 additions & 0 deletions docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.from_pyscf.rst
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@@ -0,0 +1,8 @@
:orphan:

chemcoord.Cartesian.from\_pyscf
====================================

.. currentmodule:: chemcoord

.. automethod:: Cartesian.from_pyscf
8 changes: 8 additions & 0 deletions docs/source/src_Cartesian/src_Cartesian/chemcoord.Cartesian.to_pyscf.rst
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:orphan:

chemcoord.Cartesian.to\_pyscf
===========================

.. currentmodule:: chemcoord

.. automethod:: Cartesian.to_pyscf
2 changes: 1 addition & 1 deletion src/chemcoord/_cartesian_coordinates/_cart_transformation.py
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Expand Up @@ -1095,7 +1095,7 @@
if r == 0:
return np.array([0.0, 0.0, 0.0])
alpha = arccos(-z / r)
delta = arctan2(-y / r, x / r)
delta = arctan2(-y, x)

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src/chemcoord/_cartesian_coordinates/_cart_transformation.py#L1098 

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return np.array([r, alpha, delta])


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2 changes: 1 addition & 1 deletion src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py
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Expand Up @@ -268,7 +268,7 @@
return molecule

@classmethod
def from_pyscf_molecule(cls, mol):
def from_pyscf(cls, mol):

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src/chemcoord/_cartesian_coordinates/_cartesian_class_io.py#L271 

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"""Create an instance of the own class from a PySCF molecule

Args:
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2 changes: 1 addition & 1 deletion tests/cartesian_coordinates/Cartesian/test_io.py
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Expand Up @@ -74,4 +74,4 @@ def test_xyz_cast():

def test_pyscf_conversion():
m = Cartesian.read_xyz(get_complete_path("water.xyz"))
assert allclose(Cartesian.from_pyscf_molecule(m.to_pyscf()), m)
assert allclose(Cartesian.from_pyscf(m.to_pyscf()), m)